José Carlos Rufino Amaro

Prof. Dr. José Carlos Rufino Amaro

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Research Focus & Metrics

Academic Career Length

23Years (2004-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

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11 June 2015 in Molecular Ecology
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Journal Article
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JCJulio César Chávez-Galarza
Julio César Chávez-Galarza
Dora HenriquesDora Henriques
Dora Henriques
JJJ. Spencer Johnston
J. Spencer Johnston
MCMiguel Angel Carretero
Miguel Angel Carretero
JAJosé Carlos Rufino Amaro
José Carlos Rufino Amaro
M. Alice PintoM. Alice Pinto
M. Alice Pinto
Dissecting diversity patterns of organisms endemic to Iberia has been truly challenging for a variety of taxa, and the Iberian honey bee is no exception. Surveys of genetic variation in the Iberian honey bee are among the most extensive for any honey bee subspecies. From these, differential and complex patterns of diversity have emerged, which have yet to be fully resolved. Here, we used a genome‐wide data set of 309 neutrally tested single nucleotide polymorphisms (SNPs), scattered across the 16 honey bee chromosomes, which were genotyped in 711 haploid males. These SNPs were analysed along with an intergenic locus of the mtDNA, to reveal historical patterns of population structure across the entire range of the Iberian honey bee. Overall, patterns of population structure inferred from nuclear loci by multiple clustering approaches and geographic cline analysis were consistent with two major clusters forming a well‐defined cline that bisects Iberia along a northeastern–southwestern axis, a pattern that remarkably parallels that of the mtDNA. While a mechanism of primary intergradation or isolation by distance could explain the observed clinal variation, our results are more consistent with an alternative model of secondary contact between divergent populations previously isolated in glacial refugia, as proposed for a growing list of other Iberian taxa. Despite current intense honey bee management, human‐mediated processes have seemingly played a minor role in shaping Iberian honey bee genetic structure. This study highlights the complexity of the Iberian honey bee patterns and reinforces the importance of Iberia as a reservoir ofApis melliferadiversity.

25 January 2024 in Scientific Data
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Journal Article
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AQAndreia Quaresma
Andreia Quaresma
MAMarkus J. Ankenbrand
Markus J. Ankenbrand
CGCarlos Ariel Yadró Garcia
Carlos Ariel Yadró Garcia
JAJosé Carlos Rufino Amaro
José Carlos Rufino Amaro
MHMónica Honrado
Mónica Honrado
Alexander KellerAlexander Keller
Alexander Keller
One of the most critical steps for accurate taxonomic identification in DNA (meta)-barcoding is to have an accurate DNA reference sequence dataset for the marker of choice. Therefore, developing such a dataset has been a long-term ambition, especially in the Viridiplantae kingdom. Typically, reference datasets are constructed with sequences downloaded from general public databases, which can carry taxonomic and other relevant errors. Herein, we constructed a curated (i) global dataset, (ii) European crop dataset, and (iii) 27 datasets for the EU countries for the ITS2 barcoding marker of vascular plants. To that end, we first developed a pipeline script that entails (i) an automated curation stage comprising five filters, (ii) manual taxonomic correction for misclassified taxa, and (iii) manual addition of newly sequenced species. The pipeline allows easy updating of the curated datasets. With this approach, 13% of the sequences, corresponding to 7% of species originally imported from GenBank, were discarded. Further, 259 sequences were manually added to the curated global dataset, which now comprises 307,977 sequences of 111,382 plant species.

30 March 2021 in Computational and Mathematical Organization Theory
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Journal Article
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Carlos BalsaCarlos Balsa
Carlos Balsa
ILIsabel Lopes
Isabel Lopes
Teresa GuardaTeresa Guarda
Teresa Guarda
JAJosé Carlos Rufino Amaro
José Carlos Rufino Amaro

4 November 2005
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Conference Paper
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JEJosé Exposto
José Exposto
Joaquim MacedoJoaquim Macedo
Joaquim Macedo
APAntónio Pina
António Pina
AAAlbano Alves
Albano Alves
JAJosé Carlos Rufino Amaro
José Carlos Rufino Amaro
This paper evaluates scalable distributed crawling by means of the geographical partition of the Web. The approach is based on the existence of multiple distributed crawlers each one responsible for the pages belonging to one or more previously identified geographical zones. The work considers a distributed crawler where the assignment of pages to visit is based on page content geographical scope. For the initial assignment of a page to a partition we use a simple heuristic that marks a page within the same scope of the hosting web server geographical location. During download, if the analyze of a page contents recommends a different geographical scope, the page is forwarded to the well-located web server.A sample of the Portuguese Web pages, extracted during the year 2005, was used to evaluate: a) page download communication times and the b) overhead of pages exchange among servers. Evaluation results permit to compare our approach to conventional hash partitioning strategies.

1 January 2013 in Lecture Notes in Computer Science
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Book Chapter
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AAAlbano Alves
Albano Alves
JAJosé Carlos Rufino Amaro
José Carlos Rufino Amaro
APAntónio Pina
António Pina
LSLuís Paulo Santos
Luís Paulo Santos

1 March 2019 in Apidologie
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Journal Article
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DHDora Henriques
Dora Henriques
JCJúlio Chávez-Galarza
Júlio Chávez-Galarza
AQAndreia Quaresma
Andreia Quaresma
CNCátia José Neves
Cátia José Neves
ALAna Rita Lopes
Ana Rita Lopes
M. Alice PintoM. Alice Pinto
M. Alice Pinto